​The congregation which formed St. Paul Church was originally the slave membership of Edenton Street United Methodist Church.

The Black members attended services there, but due to a rapid growth in their membership, different housing arrangements became necessary.

In 1853, White Methodists bought the Old Christ Episcopal Church, where the Blacks had been worshipping since 1846. The congregation worshipped under other names, but it was in 1848 that "St. Paul Church" was formally established.

In 1854, the Black membership moved the old church to the corner of Harrington and Edenton Streets.

The Black congregation remained under the guidance of the Methodist Episcopal Church, in the South, until Emancipation.

In 1865, the membership severed its ties with Edenton Street Methodist Church and joined the African Methodist Episcopal Church Conference, a Black denomination founded in 1787 by Richard Allen and organized in 1816.

At the South Carolina Conference of the A.M.E. Church, Bishop Daniel A. Payne appointed Rev. George A. Broadie from the Canada Conference as the pastor of St. Paul, thereby giving the church its first Black pastor, as well as establishing African Methodism in Raleigh and Wake County.​

The birth of the current structure was the result of a long building campaign which began in 1884. The church formally opened in 1901.

The Black membership desired a church comparable to other white churches in the community.

The structure is a reflection of red brick and wood, American Gothic Style Revival.

It was built by Black Masons who were renown for "the excellence of the Black mason's craft" in Raleigh during the last quarter of the 19th century.​

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The record bears that St. Paul was built by the "first independent Black congregation" formed in Raleigh. It is the oldest Black church in Wake County, North Carolina.​

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For over 100 years, St. Paul has served as the central meeting place for Blacks in Raleigh and Wake County.